breseq  version 0.29.0  revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-IND_KHP_HOT_A3_F054_I0_R1_S19_L004_R1_0013,275,249327,416,826100.0%100.0 bases100 bases97.4%
errorsqtrim-IND_KHP_HOT_A3_F054_I0_R1_S19_L004_R2_0013,275,231326,863,121100.0%99.8 bases100 bases96.7%
total6,550,480654,279,947100.0%99.9 bases100 bases97.1%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,641,652137.02.498.1%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,641,652100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 100000100000
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 4
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000648
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.029

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.55800

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 0
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 6

Read Alignment Evidence

optionvalue
ModeFull Polymorphism
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoffOFF
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff2
Polymorphism frequency cutoff0.15
Polymorphism minimum coverage each strand2
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs of ≥3 bases
Skip base substitutions when they create a homopolymer flanked on each side by ≥2 bases

Execution Times

stepstartendelapsed
Read and reference sequence file input15:50:19 14 Jan 201715:51:30 14 Jan 20171 minute 11 seconds
Read alignment to reference genome15:51:30 14 Jan 201715:54:37 14 Jan 20173 minutes 7 seconds
Preprocessing alignments for candidate junction identification15:54:37 14 Jan 201715:56:59 14 Jan 20172 minutes 22 seconds
Preliminary analysis of coverage distribution15:56:59 14 Jan 201715:59:36 14 Jan 20172 minutes 37 seconds
Identifying junction candidates15:59:36 14 Jan 201716:01:52 14 Jan 20172 minutes 16 seconds
Re-alignment to junction candidates16:01:52 14 Jan 201716:02:30 14 Jan 201738 seconds
Resolving alignments with junction candidates16:02:30 14 Jan 201716:06:24 14 Jan 20173 minutes 54 seconds
Creating BAM files16:06:24 14 Jan 201716:07:55 14 Jan 20171 minute 31 seconds
Tabulating error counts16:07:55 14 Jan 201716:10:47 14 Jan 20172 minutes 52 seconds
Re-calibrating base error rates16:10:47 14 Jan 201716:10:48 14 Jan 20171 second
Examining read alignment evidence16:10:48 14 Jan 201717:17:26 14 Jan 20171 hour 6 minutes 38 seconds
Polymorphism statistics17:17:26 14 Jan 201717:17:29 14 Jan 20173 seconds
Output17:17:29 14 Jan 201717:18:29 14 Jan 20171 minute 0 seconds
Total 1 hour 28 minutes 10 seconds